[BioC] Question about a packages not yet in Bioconductor: AffyProbeMiner in R260 under windows

[James W. MacDonald]

In addition, at the bottom of the page you reference there is this message:

If you have any problems, questions or feedback on the tool, please 
email us.

Where the 'email us' is a link that you can use to send them an email. 
So why would you ignore that source of information and instead ask a 
group of people who are completely unrelated to the project from which 
you got the package?

Anyway, I have to go finish the email I am sending to Bill Gates asking 
why my Fedora 7 box won't play Quicktime movies...

Best,

Jim



Robert Gentleman wrote:
> It looks like you are using windows and they do not provide packages for 
> windows users. The reason they are not recognized by R is that they 
> won't work.
> 
> Your options are to
> 1) install enough tools on your computer to build packages (details can 
> be found on CRAN)
> 2) use the remapped probe packages that are released through the 
> Bioconductor project for which we do have windows packages
> 
> I have no idea what the intentions of AffyProbeMiner are, they have 
> never submitted anything, and until they do, it won't even be considered,
> 
>   best wishes
>     Robert
> 
> 
> phguardiol at aol.com wrote:
>> Dear colleagues,
>>
>>
>> I m trying to use the AffyProbeMiner packages available from http://gauss.dbb.georgetown.edu/liblab/affyprobeminer/gene.html?that can replace the usual CDF probes and annotation files available in BioC.
>>
>> I m using R 2.6.0 under WinXPPro SP2.
>> I have downloaded the files available on the webpage above in the R library folder. 
>> These are gz.rar compressed files and are not recognized in R windows : Packages -> Install packages from local zip files. 
>> I have used WinRar to uncompress these files and have copy and paste the?folders (ex: hgu133ageneccds) located in the uncompressed folders (ex: hgu133ageneccds_1.1.0) in the R folder library.??
>>
>> Then if I type:
>> ?> library(hgu133ageneccds)
>>
>> I obtain the following error:
>> Error in library(hgu133ageneccds) : 
>> ? 'hgu133ageneccdscdf' is not a valid package -- installed < 2.0.0?
>> The same is true for all of these files
>>
>> Is it a problem of compatibility with R (too old files ?) ? Should I use a different way to install these packages in R 2.6.0 ?
>>
>>
>> Is there a plan to include these files and their update in BioC metadata ?
>>
>>
>> Thanks for your help
>> and hoping that this request will not be out of scope from this list since it is not a bioconductor package.
>>
>> Philippe Guardiola, MD
>>
>>
>> 	[[alternative HTML version deleted]]
>>
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>>
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623